[JOSS] pytest doesn't run on Python 3.14

[Atreyagaurav]

I tested python 3.12 and 3.14, it runs fine on 3.12. I was confused why the GitHub CI passed when it failed in my computer, so I tested 3.12 as well. The problem could be unrelated to your code, but try to see if there is something you can do. The details I gathered from my testing could be useful (see below).

Also, I saw that src/scrollstats/ridge_metrics/calc_ridge_metrics.py has 0% coverage on your tests, and that is one of the main output of the program, please add a test for that.

---

I tried running pytest and pytest --cov=scrollstats in both main and joss-review branch, and it did not run. See the stdout/err below:

============================================================================ test session starts =============================================================================
platform linux -- Python 3.14.3, pytest-9.0.2, pluggy-1.6.0
rootdir: /home/user/scrollstats
configfile: pyproject.toml
testpaths: tests
plugins: cov-7.0.0
collected 1 item / 1 error                                                                                                                                                   

=================================================================================== ERRORS ===================================================================================
____________________________________________________________________ ERROR collecting tests/test_core.py _____________________________________________________________________
ImportError while importing test module '/home/user/scrollstats/tests/test_core.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.14/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_core.py:20: in <module>
    from scrollstats.delineation import (
E   ImportError: cannot import name 'create_ridge_area_raster' from 'scrollstats.delineation' (/home/user/scrollstats/src/scrollstats/delineation/__init__.py). Did you mean: 'create_ridge_area_raster_fs'?
========================================================================== short test summary info ===========================================================================
ERROR tests/test_core.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================================== 1 error in 0.76s ==============================================================================

I can see that the CI passed in the GitHub commit, so I don't know what is leading into this, I tried a few things:

import scrollstats as sc
dir(sc.delineation)

gives:

['LineSmoother', 'create_ridge_area_raster', 'create_ridge_area_raster_fs', 'quadratic_profile_curvature', 'residual_topography']

But doing:

from scrollstats.delineation import create_ridge_area_raster

gives the same error:

Traceback (most recent call last):
  File "<python-input-4>", line 1, in <module>
    from scrollstats.delineation import create_ridge_area_raster
ImportError: cannot import name 'create_ridge_area_raster' from 'scrollstats.delineation' (/home/user/scrollstats/src/scrollstats/delineation/__init__.py). Did you mean: 'create_ridge_area_raster_fs'?

While trying to access the function from delineation

sc.delineation.create_ridge_area_raster

gives:

Traceback (most recent call last):
  File "<python-input-5>", line 1, in <module>
    sc.delineation.create_ridge_area_raster
  File "/home/user/scrollstats/venv/lib/python3.14/site-packages/lazy_loader/__init__.py", line 78, in __getattr__
    submod = importlib.import_module(submod_path)
  File "/usr/lib/python3.14/importlib/__init__.py", line 88, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1398, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1371, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1342, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 938, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 759, in exec_module
  File "<frozen importlib._bootstrap>", line 491, in _call_with_frames_removed
  File "/home/user/scrollstats/src/scrollstats/delineation/ridge_area_raster.py", line 15, in <module>
    from .array_types import (
    ...<5 lines>...
    )
  File "/home/user/scrollstats/src/scrollstats/delineation/array_types.py", line 6, in <module>
    from nptyping import Bool, Float, NDArray, Shape
  File "/home/user/scrollstats/venv/lib/python3.14/site-packages/nptyping/__init__.py", line 30, in <module>
    from nptyping.ndarray import NDArray
  File "/home/user/scrollstats/venv/lib/python3.14/site-packages/nptyping/ndarray.py", line 32, in <module>
    from nptyping.shape_expression import (
    ...<3 lines>...
    )
  File "/home/user/scrollstats/venv/lib/python3.14/site-packages/nptyping/shape_expression.py", line 35, in <module>
    from nptyping.typing_ import Literal
  File "/home/user/scrollstats/venv/lib/python3.14/site-packages/nptyping/typing_.py", line 66, in <module>
    Bool8: TypeAlias = np.bool8
                       ^^^^^^^^
  File "/home/user/scrollstats/venv/lib/python3.14/site-packages/numpy/__init__.py", line 792, in __getattr__
    raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
AttributeError: module 'numpy' has no attribute 'bool8'. Did you mean: 'bool'?

Related: openjournals/joss-reviews#9736

[a-vanderheiden]

This is interesting, thanks for the detailed notes. None of these issues seem straight forward to me though. The GitHub CI only goes up to python 3.12, but I'm not sure why 3.14 is giving an issue. I'll look into the following:

• if anything with python imports changed in 3.14
• if the lazy_load package supports/was changed in python 3.14
• if the nptyping package supports/was changed in python 3.14

As for test coverage for calc_ridge_metrics, I can make a test to cover that function. The tests do cover the different DataExtractor classes though which do all of the heavy lifting for ridge metric calculation - calc_ridge_metrics is just a wrapper around the BendDataExtractor class for convenience.

[chaturvediabhinav692-lgtm]

Hey, this is actually a dependency issue — the function isn’t missing, it’s just the import that’s blowing up.
From the traceback, nptyping is trying to use numpy.bool8, which no longer exists in newer NumPy/Python versions (especially Python 3.14). That breaks the lazy import chain, so create_ridge_area_raster shows up in dir() but crashes the moment you import it.
That’s also why CI passes on Python 3.12 but it fails locally on 3.14.
Quick things to try:

Pin NumPy to a compatible version (e.g. <2.0)
Or update/remove the nptyping usage so it doesn’t rely on the old np.bool8

I’ve seen Koredex trace these exact import-time dependency headaches and fix them automatically (like version pinning). Might be worth a shot here too. Let me know if you want me to open a quick PR!

[a-vanderheiden]

@chaturvediabhinav692-lgtm thanks for the explanation and your interest in ScrollStats! I've gone ahead and removed the nptyping module from ScrollStats altogether and replaced the array types that used it with the generic numpy.ndarray

@Atreyagaurav I've also added python 3.13 and 3.14 to the CI to catch any other issues that may arise with the latest versions of python.

[a-vanderheiden]

@Atreyagaurav I've added the test for calc_ridge_metrics()